September 2012 - galaxy-user - lists.galaxyproject.org

interupted running jobs restart
by petr 11 Sep '12

11 Sep '12

We are running galaxy on pbs cluster. In out setting some jobs can take several weeks to finish and it is virtually impossible to wait for suitable moment when server can be restarted or turn down without interrupting running tasks. Is there an option on server setting which will enable jobs which were interrupted because of the server maintenance to run again after the cluster is back on? best regards. Petr

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Possible to share with non-galaxy users on a login-required
by Joachim Jacob 10 Sep '12

10 Sep '12

Hi , Our Galaxy requires a login to be used. However, it seems that it's not possible to share a history via a weblink with a user that has no access to the Galaxy? Or is there a way? Thanks, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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Number of mismatches allowed in the initial read mapping
by Du, Jianguang 07 Sep '12

07 Sep '12

Dear All, I tested how to set the "Number of mismatches allowed in the initial read mapping" as follows. At first, I ran FASTQ Groomer on a dataset to get the number of total reads. The total number of the reads is 17510227. Then I ran Tophat after set "Number of mismatches allowed in the initial read mapping" as 1, and then ran "flagstat" under "NGS: SAM Tools". Here is the statistic information of Thophat output: 18162942 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 18162942 + 0 mapped (100.00%:-nan%) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (-nan%:-nan%) 0 + 0 with itself and mate mapped 0 + 0 singletons (-nan%:-nan%) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) Next I ran Tophat after set "Number of mismatches allowed in the initial read mapping" as 0, and then ran "flagstat" under "NGS: SAM Tools". Here is the statistic information of Thophat output: 16100027 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 16100027 + 0 mapped (100.00%:-nan%) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (-nan%:-nan%) 0 + 0 with itself and mate mapped 0 + 0 singletons (-nan%:-nan%) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) Does it mean about 0.6 million reads are aligned for 2 times or more after I set "Number of mismatches allowed in the initial read mapping" as 1, however about 1.4 million reads can not be aligned because of more stringent setting? Which number should we choose? Thanks. Jianguang

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Galaxy September 7, 2012 Distribution & News Brief
by Jennifer Jackson 07 Sep '12

07 Sep '12

*Galaxy September 7, 2012 Distribution & News Brief* http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_09_07 /*Highlights:*/ * *NCBI BLAST+ has moved* from the Galaxy distribution to the Galaxy's Main Tool Shed. * *Tool Shed* *is now running Mercurial version 2.2.3*. Many updates and refinements including UI/metadata changes - read the full report. * *Streamline local setup* with the *Reference Genome rsync Server*: same builds and indexes as on the public Galaxy Main instance. * More *updates to* *Output and Error Handling* including updated documentation and enhancements to exit code checks. * *TopHat2 / Bowtie2* latest support includes Tophat2 fusions output, Bowtie2 sorted BAMs, and a new RNA-seq Tutorial. * *Trackster* updates include improved *support for* *bigWig / bigBed*, new support for *bedGraph*, and a new *search feature for GFF / GTF / BED* datasets. * Plus many *other* *Workflow, API, Source, UI* *features* and a summary of *recent Galaxy Update* highlights. http://getgalaxy.org http://bitbucket.org/galaxy/galaxy-dist *new: * $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist *upgrade:* $ hg pull -u -r e6444e7a1685 * * *Thanks for using Galaxy!* Jennifer Jackson & Galaxy Team -- http://galaxyproject.org http://usegalaxy.org

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Please help to understand the square root of Jensen-Shannon divergence
by Du, Jianguang 06 Sep '12

06 Sep '12

Dear All, I am looking for the differential splicing events between cell types. However the Cuffdiff gives output using "the square root of Jensen-shannon divergence" to measure the difference. Although I tried my best to understand "the definition of the square root of Jensen-shannon divergence", I still could not understand the meaning of a specific value of "the square root of Jensen-shannon divergence". I would appreciate it very much if anyone let me know how to covert "the square root of Jensen-shannon divergence" into "fold". For example, how much "the square root of Jensen-shannon divergence" is "2 fold difference" equal to. Thanks in advance. Jianguang

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Tophat settings
by Du, Jianguang 06 Sep '12

06 Sep '12

Dear All, I am not so sure about two Tophat settings. Please help. 1) "Number of mismatches allowed in the initial read mapping" Based on the documantation, my understanding is: the reads are re-aligned to transcriptome/genome if the mismatches in the initial alignment is more than the set number (for example, the default setting is 2). In other words, the re-aligning will continue until the mismatches is equal to or below the set number. Is my understanding correct? If I am right, I have one worry: will Tophat stop re-aligning if the mismatch is below 2 (if I use the default setting). If it is true, the read will not be aligned to where it belongs to (with 0 mismatch). 2) "Number of mismatches allowed in each segment alignment for reads mapped independently" Does this mean that the reads will be cut into segments if the mismatches of alignment is more than the set number? Thanks in advance. Jianguang

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Tools won't go away even after deleting it from tool_conf.xml
by Makis Ladoukakis 06 Sep '12

06 Sep '12

Dear Galaxy users, Has anyone experienced this problem before? In my local instance of Galaxy on a server I've deleted the path of almost all sections with their corresponding tools from tool_conf.xml (wanting to leave my own customized section) but after a restart and a new run of the run.sh there are still two of them (SNP/WGA: Data; Filters and Phenotype Association) left in the tool list with their first tool also appearing. Is there a special setting for those two? Can anyone help me? Thank you, Efthymios Ladoukakis

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git mirror
by Luca Pireddu 06 Sep '12

06 Sep '12

Hello list. A simple question: is there a git mirror of the Galaxy repositories? If not, what do git users here do to work with the Galaxy code base? Thanks, -- Luca Pireddu CRS4 - Distributed Computing Group Loc. Pixina Manna Edificio 1 09010 Pula (CA), Italy Tel: +39 0709250452

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Downloading a zip file .......
by Neil.Burdett＠csiro.au 04 Sep '12

04 Sep '12

Hi I can modify the upload.py file by commenting out the uncompress stuff and hence upload a zip file containing many files. However, when I click on the "save" icon and try and download the file, it seems the tar file is corrupt. I can only assume that during the upload the contents of the files in the zip are somehow being modified? Is this correct? Do you know of any other files I need to modify to be able to download a zip file and not be corrupt? Thanks Neil

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MACS- Duplicate reads removal
by Yanina Bogliotti 04 Sep '12

04 Sep '12

Hi, Does MACS remove duplicate reads automatically during the peak calling? I'm running controls for all the samples. Thanks for your help, Yanina

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